Merge pull request #2271 from silx-kit/2024.09

2024.09

.github/workflows/codeql-analysis.yml

@@ -42,7 +42,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -53,7 +53,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -67,4 +67,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

.github/workflows/python-package.yml

@@ -15,12 +15,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

README.rst

@@ -98,7 +98,7 @@ Documentation can be build using this command and Sphinx (installed on your comp
 Dependencies
 ------------
 
-Python 3.7, ... 3.12 are well tested and officially supported.
+Python 3.8, ... 3.12 are well tested and officially supported.
 For full functionality of pyFAI the following modules need to be installed.
 
 * ``numpy``      - http://www.numpy.org
@@ -145,7 +145,7 @@ using apt-get these can be installed as::
 MacOSX
 ------
 
-One needs to manually install a recent version of `Python` (>=3.7) prior to installing pyFAI.
+One needs to manually install a recent version of `Python` (>=3.8) prior to installing pyFAI.
 Apple provides only an outdated version of Python 2.7 which is now incomatible.
 If you want to build pyFAI from sources, you will also need `Xcode` which is available from the Apple store.
 The compiled extension will use only one core due to the limitation of the compiler.
@@ -158,7 +158,7 @@ Then install the missing dependencies with `pip`::
 Windows
 -------
 
-Under Windows, one needs to install `Python` (>=3.7) prior to pyFAI.
+Under Windows, one needs to install `Python` (>=3.8) prior to pyFAI.
 The Visual Studio C++ compiler is also needed when building from sources.
 Then install the missing dependencies with `pip`::
 

doc/source/changelog.rst

@@ -1,12 +1,46 @@
 :Author: Jérôme Kieffer
-:Date: 21/05/2024
+:Date: 12/09/2024
 :Keywords: changelog
 
 Change-log of versions
 ======================
 
-2024.5 21/05/2024
------------------
+2024.09 12/09/2024
+------------------
+- New tutorials:
+  + On flatfield calculation from several detector position (ID31)
+  + On dynamic masks when using sigma-clipping (ID15a)
+- New feature in pilx: the tool to view diffraction map
+  + fix/unfix curves
+  + Colors improved
+  + motor position can ge registered
+- Other new feature:
+  + Expose orientation in calib2
+  + Extra comments in PONI-file like the calibration file if available
+  + implement sigma-clipping in pure cython with hybrid error-model
+  + New calibrant (Lysozyme for MX)& integration into calib2
+  + Absorption kwarg in sigma-clip was missing
+  + Engineering notation when printing pixel size
+  + New JSON format for integration configuration (backward compatible)
+  + Import CrystFEL geom-file and generate a detector + geometry
+  + GIWAXS and sigma-clip impose *no* pixel splitting
+  + Sigma-clipping is possible from the GUI and via config files
+  + Peakfinding: discard peaks with masked pixels in the local region
+- New detector: Jungfrau 1M (ID09)
+- Bug fixed:
+  + Close HDF5 files ASAP (risk of hitting the max number of file open)
+  + Bug in medfilt (empty ensemble)
+  + Several bugs fixed in worker (heavily used by ewoks)
+  + Correct some tutorials which had typos
+  + Orientation of interate2d results *legacy* vs *ng*
+  + Compatibility with Numpy2
+  + Compatibility with Eiger2+Lima2 multi-threshold files
+  + Compatibility with GCC14, discarded some deprecated code
+- Validated with Python 3.8-3.12
+
+
+2024.05 21/05/2024
+------------------
 - Implemented unweighted average for 2D integration
  + Integration engines now handle the boolean 'weighted_average' to switch to unweighted mean, similar to legacy methods
 - Implementation of pilx (pyFAI-diffmap-view command): interactive viewer for pyFAI-diffmap files (thanks Loic Huder)
@@ -19,16 +53,16 @@ Change-log of versions
 - Build system moved from bob to cibuildwheels
   + Windows wheels are build with openmp disabled
 
-2024.2 01/02/2024
------------------
+2024.02 01/02/2024
+------------------
 - Include grazing-incidence capabilities + tutorial (thanks Edgar)
 - Fix segmentation-fault in calib2 application #2047 (thanks Thomas & Edgar)
 - Use the dynamic mask to mask-out dead pixels in Eiger images in calib2
 - Extend Poisson+azimuthal uncertainties to all Cython integrators (+ non regression tests)
 - Support for Python 3.7-3.12 (requires silx v2 for 3.12)
 
-2024.1 18/01/2024
------------------
+2024.01 18/01/2024
+------------------
 - Possibility to define the detector orientation:
   + It is the position of the origin of the detector at any of the 4 corners of the image
   + Uses the EXIF nomenclature where pyFAI's (default) orientation is tagged *3*

doc/source/operations/index.rst

@@ -1,5 +1,5 @@
 :Author: Jérôme Kieffer
-:Date: 18/01/2023
+:Date: 12/09/2024
 :Keywords: Installation procedure
 :Target: System administrators
 
@@ -22,7 +22,7 @@ Dependencies
 
 PyFAI is a Python library which relies on the scientific stack (numpy, scipy, matplotlib)
 
-* Python: version 3.7 or newer (version 3.6 was dropped with 0.21)
+* Python: version 3.8 or newer
 * NumPy: version 1.12 or newer
 * SciPy: version 0.18 or newer
 * Matplotlib: verson 2.0 or newer

doc/source/operations/macosx.rst

@@ -11,7 +11,7 @@ Install Python3:
 
 To install pyFAI on an *Apple* computer you will need a scientific Python3 stack.
 MacOSX provides by default Python2.7, you will need to install a recent version
-of Python3 (3.7 at least).
+of Python3 (3.8 at least).
 Those distribution are available as *dmg* images from:
 `Python.org <https://www.python.org/downloads/mac-osx/>`_
 

doc/source/usage/tutorial/Calibrant/hydrocerussite.ipynb

@@ -23,7 +23,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "pyFAI version 2023.9.0-dev0\n"
+      "pyFAI version 2024.9.0-dev0\n"
      ]
     }
    ],
@@ -267,7 +267,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

doc/source/usage/tutorial/Calibrant/make_calibrant.ipynb

@@ -51,7 +51,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "using pyFAI version:  2023.9.0-dev0\n",
+      "using pyFAI version:  2024.9.0-dev0\n",
       "\n",
       "    This is a cell object, able to calculate the volume and d-spacing according to formula from:\n",
       "\n",
@@ -229,8 +229,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPU times: user 727 ms, sys: 11.4 ms, total: 739 ms\n",
-      "Wall time: 738 ms\n",
+      "CPU times: user 933 ms, sys: 8.38 ms, total: 942 ms\n",
+      "Wall time: 941 ms\n",
       "Number of reflections: 1441\n"
      ]
     }
@@ -415,8 +415,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[<function Cell.set_type.<locals>.<lambda> at 0x7fa8208cae80>, <function Cell.set_type.<locals>.<lambda> at 0x7fa8208ca660>, <function Cell.diamond.<locals>.<lambda> at 0x7fa8208caf20>]\n",
-      "[<function Cell.set_type.<locals>.<lambda> at 0x7fa8208cb2e0>, <function Cell.set_type.<locals>.<lambda> at 0x7fa8208cb060>]\n"
+      "[<function Cell.set_type.<locals>.<lambda> at 0x7f8a468bee60>, <function Cell.set_type.<locals>.<lambda> at 0x7f8a468bedd0>, <function Cell.diamond.<locals>.<lambda> at 0x7f8a468bf0a0>]\n",
+      "[<function Cell.set_type.<locals>.<lambda> at 0x7f8a468bf2e0>, <function Cell.set_type.<locals>.<lambda> at 0x7f8a468bef80>]\n"
      ]
     }
    ],
@@ -489,7 +489,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

doc/source/usage/tutorial/Calibrant/new_calibrant.ipynb

@@ -23,7 +23,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "pyFAI version 2023.9.0-dev0\n"
+      "pyFAI version 2024.9.0-dev0\n"
      ]
     }
    ],
@@ -197,7 +197,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,